Crash in Qt cleanup during garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x0000000204ff0600 (most recent call first):
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 376 in _cleanup
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 416 in cb
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 38000,
  "procLaunch" : "2022-07-04 18:59:17.1708 +0200",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,4",
  "procStartAbsTime" : 909534437740,
  "coalitionID" : 6993,
  "osVersion" : {
    "train" : "macOS 12.2.1",
    "build" : "21D62",
    "releaseType" : "User"
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  "captureTime" : "2022-07-04 19:10:09.4590 +0200",
  "incident" : "E1FBE492-6716-439E-B4EE-D59EC8346C01",
  "bug_type" : "309",
  "pid" : 16956,
  "procExitAbsTime" : 925188888978,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"F1C621B2-C7E5-561A-A374-FF6BE21194D8","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "39466E2D-B7FF-4C2F-9031-9995675C174F",
  "wakeTime" : 1813,
  "sleepWakeUUID" : "44086599-D970-488B-81E7-44C82D8C0538",
  "sip" : "enabled",
  "vmRegionInfo" : "0x7700f8889288 is not in any region.  Bytes after previous region: 25291863397001  Bytes before following region: 9388067089784\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_NANO (reserved)   600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)\n--->  GAP OF 0x1f8a8cf00000 BYTES\n      MALLOC_LARGE             7f8accf00000-7f8acd990000 [ 10.6M] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000f700f8889288","rawCodes":[1,271583541760648],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000f700f8889288 -> 0x00007700f8889288 (possible pointer authentication failure)"},
  "vmregioninfo" : "0x7700f8889288 is not in any region.  Bytes after previous region: 25291863397001  Bytes before following region: 9388067089784\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_NANO (reserved)   600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)\n--->  GAP OF 0x1f8a8cf00000 BYTES\n      MALLOC_LARGE             7f8accf00000-7f8acd990000 [ 10.6M] rw-\/rwx SM=PRV  ",
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  "faultingThread" : 0,
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/carolin/OneDrive - TUM/PhD/ChimeraSessions/AF-hEMC.cxs" format
> session

opened ChimeraX session  

> open /Users/carolin/Downloads/AF-P27824-F1-model_v2.pdb

AF-P27824-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for calnexin (P27824) [more info...]  
  
Chain information for AF-P27824-F1-model_v2.pdb #2  
---  
Chain | Description | UniProt  
A | calnexin | CALX_HUMAN  
  

> ui tool show XMAS

  
Peptide pair mapping of XlinkX evidence file:
/Users/carolin/Library/CloudStorage/OneDrive-
TUM/PhD/MS/202207_EMCCanxPhoX_take2/20220629_EXPL6_BaSt_SA_LC12_19_Orbi4270_Sample01_Crosslinks.txt  
Unique peptide pairs: 368 out of 368  
Unique peptide pairs with pseudobonds: 351  
Pseudobonds are stored in /Users/carolin/Library/CloudStorage/OneDrive-
TUM/PhD/MS/202207_EMCCanxPhoX_take2/20220629_EXPL6_BaSt_SA_LC12_19_Orbi4270_Sample01_Crosslinks_1,2.pb  
Mapping information is stored in /Users/carolin/Library/CloudStorage/OneDrive-
TUM/PhD/MS/202207_EMCCanxPhoX_take2/20220629_EXPL6_BaSt_SA_LC12_19_Orbi4270_Sample01_Crosslinks_1,2.tsv  
Drag select of 26 atoms  

> hide sel atoms

> show sel cartoons

> hide sel atoms

> show sel cartoons

> hide sel atoms

> hide #1 models

> show #1 models

> show sel atoms

> hide sel atoms

> show sel cartoons

> hide #3 models

> select add #1

41248 atoms, 41704 bonds, 88 pseudobonds, 2615 residues, 2 models selected  

> select subtract #1

Nothing selected  

> hide atoms

> show cartoons

> select add #2

4759 atoms, 4886 bonds, 149 pseudobonds, 592 residues, 2 models selected  

> ui mousemode right "translate selected models"

Drag select of 18 residues  

> select add #2

4759 atoms, 4886 bonds, 149 pseudobonds, 592 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #2

4759 atoms, 4886 bonds, 149 pseudobonds, 592 residues, 2 models selected  

> view matrix models
> #2,1,0,0,50.21,0,1,0,-90.225,0,0,1,5.8606,#3,1,0,0,0,0,1,0,0,0,0,1,0

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.22378,-0.96428,-0.1417,30.841,-0.64013,0.03578,0.76743,-110.28,-0.73495,0.26244,-0.62528,12.385,#3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #2,0.5585,-0.75181,-0.35051,37.223,-0.73154,-0.64562,0.21917,-120.55,-0.39107,0.13401,-0.91055,11.971,#3,1,0,0,0,0,1,0,0,0,0,1,0

> show #3 models

> select add #3

4759 atoms, 4886 bonds, 340 pseudobonds, 592 residues, 2 models selected  

> select subtract #3

4759 atoms, 4886 bonds, 592 residues, 1 model selected  

> view matrix models
> #2,0.54926,-0.55114,-0.62814,41.291,-0.51525,-0.81515,0.26468,-122.89,-0.6579,0.17828,-0.7317,11.473

> view matrix models
> #2,0.91765,0.075266,-0.3902,52.255,0.16822,-0.96316,0.20982,-123.25,-0.36003,-0.25818,-0.8965,5.4397

> view matrix models
> #2,0.98043,-0.19402,-0.033301,46.982,-0.18319,-0.96113,0.20659,-124.23,-0.07209,-0.19645,-0.97786,7.5238

> view matrix models
> #2,0.93871,-0.26816,-0.21659,46.096,-0.29592,-0.94916,-0.10736,-123.53,-0.17679,0.16487,-0.97034,13.267

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.93871,-0.26816,-0.21659,30.469,-0.29592,-0.94916,-0.10736,-77.17,-0.17679,0.16487,-0.97034,27.19

> view matrix models
> #2,0.93871,-0.26816,-0.21659,38.158,-0.29592,-0.94916,-0.10736,8.6224,-0.17679,0.16487,-0.97034,66.844

> view matrix models
> #2,0.93871,-0.26816,-0.21659,28.413,-0.29592,-0.94916,-0.10736,-25.186,-0.17679,0.16487,-0.97034,74.165

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.2842,-0.80017,-0.52817,18.397,-0.93739,-0.34757,0.022167,-17.284,-0.20131,0.4888,-0.84885,79.215

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.2842,-0.80017,-0.52817,24.076,-0.93739,-0.34757,0.022167,-14.861,-0.20131,0.4888,-0.84885,42.549

> view matrix models
> #2,0.2842,-0.80017,-0.52817,28.056,-0.93739,-0.34757,0.022167,-13.472,-0.20131,0.4888,-0.84885,41.561

> ui mousemode right translate

> select subtract #2

Nothing selected  

> select add #1

41248 atoms, 41704 bonds, 88 pseudobonds, 2615 residues, 2 models selected  

> color sel bychain

> select subtract #1

Nothing selected  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,4
      Processor Name: Unknown
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 2 days 4:12

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    et-xmlfile: 1.1.0
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openpyxl: 3.0.10
    openvr: 1.16.802
    packaging: 21.0
    pandas: 1.4.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    seaborn: 0.11.2
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0